BN1741 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 4.1552e-05 2.7178e-04
Layer 3 4.7172e-04 1.4382e-02
Layer 5 1.1132e-03 5.6788e-03
Layer 2 1.1203e-03 2.0793e-02
Layer 6 3.3805e-03 5.7352e-03
Layer 1 4.3084e-01 4.2155e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 3.0195 0.6384
SNRPN Layer 4 2.9570 0.6145
STMN1 Layer 4 2.9863 0.5953
ATP5F1B Layer 4 2.9609 0.5861
STXBP1 Layer 4 3.0449 0.5715
ENO2 Layer 4 3.0996 0.5679
RTN3 Layer 4 2.6133 0.5669
SYP Layer 4 2.7305 0.5638
DNM1 Layer 4 2.8652 0.5636
SERPINI1 Layer 4 2.6543 0.5595
CALM3 Layer 4 2.4453 0.5509
CALY Layer 4 2.6719 0.5504
RTN1 Layer 4 2.7939 0.5454
H1FX Layer 4 2.6602 0.5450
PRKAR1B Layer 4 2.6895 0.5439
INPP5F Layer 4 2.7217 0.5435
CALM2 Layer 4 2.1816 0.5412
CAMTA1 Layer 4 2.9697 0.5399
SH3GL2 Layer 4 2.3809 0.5389
TUBA4A Layer 4 2.4844 0.5383
CLSTN1 Layer 4 2.6455 0.5379
PPP3CA Layer 4 2.6543 0.5377
HPCA Layer 4 3.2969 0.5375
PKM Layer 4 2.6367 0.5375
HSP90AB1 Layer 4 2.2324 0.5367
TSPAN7 Layer 4 2.3340 0.5343
NDRG4 Layer 4 2.8652 0.5342
NCDN Layer 4 2.9082 0.5335
SEPTIN7 Layer 4 2.5117 0.5331
TAGLN3 Layer 4 2.5332 0.5321
MORF4L1 Layer 4 2.8398 0.5320
INA Layer 4 2.4512 0.5309
CFL1 Layer 4 2.5840 0.5304
RORB Layer 4 3.2930 0.5302
TUBB Layer 4 2.6836 0.5301
PREPL Layer 4 2.8340 0.5300
SERINC1 Layer 4 2.7852 0.5298
YWHAG Layer 6 2.8027 0.5284
SPTAN1 Layer 4 2.8486 0.5282
GRIN1 Layer 4 2.8223 0.5282
NREP Layer 4 2.2744 0.5279
UCHL1 Layer 6 2.4297 0.5279
EIF4A2 Layer 4 2.6777 0.5275
EIF4G2 Layer 6 2.4150 0.5269
NGRN Layer 4 2.7100 0.5266
CHGA Layer 4 2.6309 0.5257
BASP1 Layer 4 2.4883 0.5241
CLIP3 Layer 4 2.5117 0.5240
FAIM2 Layer 4 2.9609 0.5237
NORAD Layer 4 2.5000 0.5228

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1741
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1741_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1741/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1741/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1741/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1741/report/PD/BN1741_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1741/report/PD/BN1741_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:27:39
  • Number of Processes: 10
  • Spending Time: 0h 4m